After making a change, optionally check the box: Reload windows to apply changes now.
If you check this box, then Mail Tweak will try to apply your changes immediately,
and Thunderbird's main windows will be reset.
Alternatively, restart Thunderbird after making changes.

Note: Reloading the Compose window does not always work, because
Thunderbird might reuse an old Compose window that has not loaded the new settings.
To work around this, restart Thunderbird.